first commit

inputs

@@ -46,9 +46,9 @@
 	"{{ project_name }}.qualimapBAMqc_docker": "{{ qualimapBAMqc_docker }}",
 	"{{ project_name }}.qualimapBAMqc_cluster_config": "{{ qualimapBAMqc_cluster_config }}",
 	"{{ project_name }}.qualimapBAMqc_disk_size": "{{ qualimapBAMqc_disk_size }}",
-	"{{ project_name }}.qualimapRNAseqqc_docker": "{{ qualimapRNAseqqc_docker }}",
-	"{{ project_name }}.qualimapRNAseqqc_cluster_config": "{{ qualimapRNAseqqc_cluster_config }}",
-	"{{ project_name }}.qualimapRNAseqqc_disk_size": "{{ qualimapRNAseqqc_disk_size }}",
+	"{{ project_name }}.qualimapRNAseq_docker": "{{ qualimapRNAseq_docker }}",
+	"{{ project_name }}.qualimapRNAseq_cluster_config": "{{ qualimapRNAseq_cluster_config }}",
+	"{{ project_name }}.qualimapRNAseq_disk_size": "{{ qualimapRNAseq_disk_size }}",
 	"{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
 	"{{ project_name }}.fastqscreen_cluster_config": "{{ fastqscreen_cluster_config }}",
 	"{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",

workflow.wdl

@@ -31,8 +31,8 @@ workflow {{ project_name }} {
 	String hisat2_cluster
 	String qualimapBAMqc_docker
 	String qualimapBAMqc_cluster_config
-	String qualimapRNAseqqc_docker
-	String qualimapRNAseqqc_cluster_config
+	String qualimapRNAseq_docker
+	String qualimapRNAseq_cluster_config
 	String samtools_docker
 	String samtools_cluster
 	String stringtie_docker
@@ -59,7 +59,7 @@ workflow {{ project_name }} {
 	Int fastqc_disk_size
 	Int fastqscreen_disk_size
 	Int qualimapBAMqc_disk_size
-	Int qualimapRNAseqqc_disk_size
+	Int qualimapRNAseq_disk_size
 	Int insert_size
 	Int minimum_length_allowed_for_the_predicted_transcripts
     Int Junctions_no_spliced_reads
@@ -145,9 +145,9 @@ workflow {{ project_name }} {
 		call qualimapRNAseq.qualimapRNAseq as qualimapRNAseq {
 		input:
 		bam = samtools.out_percent,
-		docker = qualimapRNAseqqc_docker,
-		cluster = qualimapRNAseqqc_cluster_config,
-		disk_size = qualimapRNAseqqc_disk_size,
+		docker = qualimapRNAseq_docker,
+		cluster = qualimapRNAseq_cluster_config,
+		disk_size = qualimapRNAseq_disk_size,
 		gtf = gtf
 		}